Variant report

Variant	rs2066557
Chromosome Location	chr13:50610270-50610271
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr13:50605656..50608518-chr13:50609379..50612153,2	K562	blood:
2	chr13:50600414..50602696-chr13:50608874..50610532,2	K562	blood:
3	chr13:50607650..50610323-chr13:51484436..51486614,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000233672	Chromatin interaction

Extended variants
information (count: 46 )
Associated
traits (count: 13 )

rSNPs within LD-proxies of this variant (count:41)

rs_ID	r²[population]
rs11617754	0.86[CHB][hapmap];0.87[CHD][hapmap];0.87[JPT][hapmap]
rs11839292	0.83[YRI][hapmap]
rs2066549	1.00[CHB][hapmap];0.91[JPT][hapmap];0.93[ASN][1000 genomes]
rs2066558	0.94[ASN][1000 genomes]
rs2066571	0.83[ASN][1000 genomes]
rs2066572	0.93[ASN][1000 genomes]
rs2066575	1.00[CHB][hapmap];1.00[CHD][hapmap];0.90[JPT][hapmap];0.91[ASN][1000 genomes]
rs2066581	0.82[YRI][hapmap]
rs2066585	1.00[CHB][hapmap];0.91[JPT][hapmap];0.88[ASN][1000 genomes]
rs2066587	0.85[ASN][1000 genomes]
rs2066591	1.00[CHB][hapmap];0.91[JPT][hapmap];0.81[ASN][1000 genomes]
rs2242482	1.00[CHB][hapmap];0.97[CHD][hapmap];0.86[JPT][hapmap];0.91[ASN][1000 genomes]
rs2687950	1.00[CHB][hapmap];0.90[JPT][hapmap]
rs2687951	1.00[CHB][hapmap];0.91[JPT][hapmap]
rs2740508	0.87[ASN][1000 genomes]
rs2740524	0.90[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];0.93[AFR][1000 genomes];0.91[AMR][1000 genomes];0.83[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2740544	0.95[CHB][hapmap];0.97[CHD][hapmap];0.90[JPT][hapmap];0.93[ASN][1000 genomes]
rs2740545	1.00[CHB][hapmap];0.90[JPT][hapmap];0.93[ASN][1000 genomes]
rs2760911	0.83[YRI][hapmap]
rs2760914	1.00[CHB][hapmap];0.97[CHD][hapmap];0.91[JPT][hapmap];0.93[ASN][1000 genomes]
rs2803839	1.00[CHB][hapmap];0.97[CHD][hapmap];0.91[JPT][hapmap];0.88[ASN][1000 genomes]
rs2812216	0.81[ASN][1000 genomes]
rs2812222	1.00[CHB][hapmap];0.91[JPT][hapmap];0.81[ASN][1000 genomes]
rs2997624	0.84[ASN][1000 genomes]
rs4548769	1.00[CHB][hapmap];0.86[JPT][hapmap]
rs4942899	1.00[CHB][hapmap];0.97[CHD][hapmap];0.91[JPT][hapmap]
rs4942901	0.83[ASN][1000 genomes]
rs790943	0.86[CHB][hapmap];0.87[JPT][hapmap];0.85[ASN][1000 genomes]
rs7986337	0.82[CHB][hapmap];0.85[CHD][hapmap];0.87[JPT][hapmap]
rs9535407	1.00[ASW][hapmap];0.86[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.94[TSI][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.85[ASN][1000 genomes]
rs9535411	0.83[YRI][hapmap]
rs9535414	0.83[YRI][hapmap]
rs9535416	0.83[YRI][hapmap]
rs9568354	1.00[ASW][hapmap];0.81[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.93[LWK][hapmap];0.90[MKK][hapmap];0.85[TSI][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.84[ASN][1000 genomes]
rs9568357	0.86[CHB][hapmap];0.85[CHD][hapmap];0.83[JPT][hapmap]
rs9568363	0.82[ASN][1000 genomes]
rs9568364	0.82[ASN][1000 genomes]
rs9568366	0.90[CHB][hapmap];0.84[CHD][hapmap];0.86[JPT][hapmap]
rs9596215	0.81[ASN][1000 genomes]
rs9596219	1.00[CHB][hapmap];0.97[CHD][hapmap];0.91[JPT][hapmap];0.88[ASN][1000 genomes]
rs9596220	1.00[CHB][hapmap];0.97[CHD][hapmap];0.91[JPT][hapmap];0.88[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1035151	chr13:50513535-51167850	Weak transcription Flanking Active TSS Strong transcription Enhancers Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	1254 gene(s)	inside rSNPs	diseases
2	esv2753964	chr13:50545399-51421199	Flanking Active TSS Enhancers Bivalent Enhancer Weak transcription Active TSS Genic enhancers Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	1256 gene(s)	inside rSNPs	diseases
3	esv2753492	chr13:50550081-51461720	Enhancers Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Weak transcription Strong transcription Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	1256 gene(s)	inside rSNPs	diseases
4	esv2752608	chr13:50550099-51054499	Weak transcription Enhancers Strong transcription Active TSS Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	1249 gene(s)	inside rSNPs	diseases
5	nsv1054415	chr13:50598121-50650938	Strong transcription Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	1202 gene(s)	inside rSNPs	diseases

mRNA abundance (count:13)

SNP	Gene	Cis/trans	Tissue	Source
rs2066557	NUDT5	trans	parietal	SCAN
rs2066557	TRIM13	Cis_1M	lymphoblastoid	RTeQTL
rs2066557	DLEU2	Cis_1M	lymphoblastoid	RTeQTL
rs2066557	RFP2	cis	multi-tissue	Pritchard
rs2066557	C13orf1	cis	cerebellum	SCAN
rs2066557	PCDH8	cis	parietal	SCAN
rs2066557	TRIM13	cis	cerebellum	SCAN
rs2066557	RB1	cis	cerebellum	SCAN
rs2066557	KDM1B	trans	parietal	SCAN
rs2066557	KCNRG	cis	cerebellum	SCAN
rs2066557	ALG11	cis	cerebellum	SCAN
rs2066557	DLEU2	cis	multi-tissue	Pritchard
rs2066557	TMEM43	trans	parietal	SCAN

Chromatin state (count:85 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr13:50578600-50629800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
2	chr13:50578800-50654400	Weak transcription	Esophagus	oesophagus
3	chr13:50586800-50654200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
4	chr13:50587000-50633800	Weak transcription	Hela-S3	cervix
5	chr13:50587000-50645600	Weak transcription	Spleen	Spleen
6	chr13:50587200-50617000	Weak transcription	HepG2	liver
7	chr13:50588000-50645600	Weak transcription	Ovary	ovary
8	chr13:50589800-50645600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
9	chr13:50590000-50624200	Weak transcription	Primary T helper cells PMA-I stimulated	--
10	chr13:50590200-50653600	Weak transcription	Small Intestine	intestine
11	chr13:50593000-50618600	Weak transcription	HMEC	breast
12	chr13:50594600-50622600	Weak transcription	A549	lung
13	chr13:50594600-50635000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
14	chr13:50594800-50616400	Weak transcription	Primary hematopoietic stem cells	blood
15	chr13:50594800-50641000	Weak transcription	Lung	lung
16	chr13:50594800-50643200	Weak transcription	Brain Hippocampus Middle	brain
17	chr13:50594800-50643600	Weak transcription	Duodenum Smooth Muscle	Duodenum
18	chr13:50595000-50615600	Weak transcription	Rectal Mucosa Donor 29	rectum
19	chr13:50595000-50617200	Weak transcription	Fetal Heart	heart
20	chr13:50595000-50654200	Weak transcription	Skeletal Muscle Male	skeletal muscle
21	chr13:50595200-50640000	Weak transcription	Rectal Mucosa Donor 31	rectum
22	chr13:50595800-50616000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
23	chr13:50595800-50616200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
24	chr13:50595800-50654400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
25	chr13:50596400-50620400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
26	chr13:50596800-50614000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
27	chr13:50596800-50615600	Weak transcription	Duodenum Mucosa	Duodenum
28	chr13:50597000-50624600	Weak transcription	Fetal Lung	lung
29	chr13:50598200-50616200	Weak transcription	Fetal Muscle Leg	muscle
30	chr13:50598200-50629800	Weak transcription	Primary T helper cells fromperipheralblood	blood
31	chr13:50598200-50634800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
32	chr13:50598200-50641000	Weak transcription	Brain Inferior Temporal Lobe	brain
33	chr13:50598400-50616800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
34	chr13:50598600-50612400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
35	chr13:50598600-50626000	Weak transcription	Primary T cells fromperipheralblood	blood
36	chr13:50598600-50627800	Weak transcription	Brain Germinal Matrix	brain
37	chr13:50598600-50640000	Weak transcription	Placenta	Placenta
38	chr13:50598600-50650200	Weak transcription	Sigmoid Colon	Sigmoid Colon
39	chr13:50598800-50612400	Weak transcription	Fetal Stomach	stomach
40	chr13:50598800-50616000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
41	chr13:50598800-50616200	Weak transcription	Fetal Muscle Trunk	muscle
42	chr13:50599000-50614200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
43	chr13:50599200-50616200	Weak transcription	Brain Angular Gyrus	brain
44	chr13:50599400-50612600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
45	chr13:50599400-50614000	Weak transcription	HSMM	muscle
46	chr13:50599800-50613800	Weak transcription	NHDF-Ad	bronchial
47	chr13:50599800-50615800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
48	chr13:50600000-50612400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
49	chr13:50600800-50616000	Weak transcription	Thymus	Thymus
50	chr13:50601200-50612400	Weak transcription	Fetal Intestine Small	intestine

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